Schmoho

**Describe the bug** After the run of a continuous replication update the container does not resume logging on the Apache process **To Reproduce** Steps to reproduce the behavior: 1. ```yml...

setup.py install_packages is broken

1

The version ranges are not specific enough, running setup.py on a blank conda env with just python 3.7 installed yields a dependency resolution error because a jupyter version > 6...

--replaces-process fails when keeping triggering button pressed

2

Obviously this is an integration issue, so I'll have to mention some context on other programs, I hope you'll bear with me. The setup is using sxhkd with the following...

Test to reproduce: ```java @Test public void test() { var m = new Model(3,2); var fbcPlugin = (FBCModelPlugin) m.getPlugin(FBCConstants.shortLabel); var o1 = fbcPlugin.createObjective("obj1"); fbcPlugin.setActiveObjective(o1); fbcPlugin.getListOfObjectives().removeAll(fbcPlugin.getListOfObjectives()); assertTrue(fbcPlugin.isSetActiveObjective()); assertEquals("obj1", fbcPlugin.getActiveObjective()); assertEquals(0, fbcPlugin.getObjectiveCount());...

update README and Wiki

1

The documentation is not very inviting currently. - in the first paragraph we greet the user with a troubleshooting hint -> can be moved to a troubleshooting page in the...

The lack of unit tests makes refactorings of any kind somewhat dangerous. Also there is significant documentation value to be had here. This issue serves to bundle commits that introduce...

the way we check for FBC strict is not compliant with the spec

4

From the [spec](https://sbml.org/specifications/sbml-level-3/version-1/fbc/sbml-fbc-version-2-release-1.pdf) section 3.3 page 8 (line numbers at the end): > This is accomplished by defining a set of restrictions which come into effect if strict is set...

Looking over the javadocs #116 revealed that we have a distinct lack of docstrings in the code base. All classes, public constructors and public methods should carry a docstring.

Extend TreeNodeWithChangeSupport with Visitor pattern

1

This is a suggestion: It seems to me that the current implementation does not support the idiomatic way to perform tree walks in Java, because the TreeNode interface that is...

Per the [specification 3.1](https://raw.githubusercontent.com/combine-org/combine-specifications/main/specifications/files/sbml.level-3.version-1.core.release-3.pdf) (and 3.2 for that matter) the ID attribute is mandatory on both entities. I.e. if an ID is missing, the SBML is not valid. In an...